Difference between revisions of "Sandbox"

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* '''Description:''' protein phosphatase <br/><br/>
+
* '''Description:''' ribulose 5-phosphate 3-epimerase <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''prpC''
+
|''rpe''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yloO ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yloR ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || protein phosphatase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ribulose 5-phosphate 3-epimerase
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || antagonist of [[PrkC]]-dependent phosphorylation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || pentose phosphate pathway
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 4.355  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 5.651  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 651 bp, 217 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yloN]]'', ''[[prkC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cpgA]]'', ''[[yloS]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14345&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13452&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:prpC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rpe_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
Line 43: Line 43:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13390]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13393]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
* '''Protein family:'''
+
* '''Protein family:''' ribulose-phosphate 3-epimerase family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 
=== Proteins dephosphorylated by PrpC ===
 
 
[[CpgA]],  [[tufA | EF-Tu]], [[YezB]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246764 PubMed], [[ptsH | HPr]] [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537  PubMed]
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 82: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34779 O34779]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34557 O34557]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15760]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU15790]
  
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.3.16 3.1.3.16]
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/5.1.3.1 5.1.3.1]
  
 
=== Additional information===
 
=== Additional information===
Line 122: Line 118:
 
=References=
 
=References=
  
# Obuchowski, M., Madec, E., Delattre, D., Boël, G., Iwanicki, A., Foulger, D. and Séror, S. J. 2000. Characterization of PrpC from ''Bacillus subtilis'', a member of the PPM phosphatase family. J. Bacteriol. 182: 5634-5638. [http://www.ncbi.nlm.nih.gov/sites/entrez/10986276 PubMed]
 
# Gaidenko TA, Kim TJ, Price CW: (2002) The PrpC serine-threonine phosphatase and PrkC kinase have opposing physiological roles in stationary-phase Bacillus subtilis cells. J Bacteriol, 184:6109-6114. [http://www.ncbi.nlm.nih.gov/sites/entrez/12399479 PubMed]
 
# Singh, K. D., Schmalisch, M. H., Stülke, J. & Görke, B. (2008) Carbon catabolite repression in Bacillus subtilis: A quantitative analysis of repression exerted by different carbon sources. J. Bacteriol. 190: 7275-7284. [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537  PubMed]
 
# Absalon C, Obuchowski M, Madec E, Delattre D, Holland IB, Séror SJ (2009) CpgA, EF-Tu and the stressosome protein YezB are substrates of the Ser/Thr kinase/phosphatase couple, PrkC/PrpC, in ''Bacillus subtilis''. ''Microbiology'' '''155:''' 932-943. [http://www.ncbi.nlm.nih.gov/sites/entrez/19246764 PubMed]
 
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 23:02, 11 May 2009

  • Description: ribulose 5-phosphate 3-epimerase

Gene name rpe
Synonyms yloR
Essential no
Product ribulose 5-phosphate 3-epimerase
Function pentose phosphate pathway
MW, pI 23 kDa, 5.651
Gene length, protein length 651 bp, 217 aa
Immediate neighbours cpgA, yloS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
Rpe context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: ribulose-phosphate 3-epimerase family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [2]

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed